# Install mmseqs2 with Homebrew, apt, Nix Software suite for very fast sequence search and clustering. Version 18-8cc5c via Homebrew; verified from local package data. ## Install ```sh sudo av install brew:mmseqs2 ``` Additional install commands: ### macOS - Homebrew (100%): ```sh brew install mmseqs2 ``` Evidence: local Homebrew formula metadata ### Linux - Debian apt (92%): ```sh sudo apt install mmseqs2 ``` Evidence: Debian stable package indexes: mmseqs2 from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz - Nix (92%): ```sh nix profile install nixpkgs#mmseqs2 ``` Evidence: nixpkgs package indexes: pkgs/by-name/mm/mmseqs2/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1 ## Package facts - **Package key:** brew:mmseqs2 - **Package manager:** Homebrew - **Package manager page:** - **Version:** 18-8cc5c - **Source summary:** Software suite for very fast sequence search and clustering - **Homepage:** - **Repository:** - **Upstream docs:** - **License:** MIT - **Source archive:** - **Generated:** 2026-07-08T07:18:31+00:00 ## Executables - mmseqs (cli) - mmseqs (alias) ## Dependencies - libomp - wget ## Build dependencies - cmake ## Uses from macOS - bzip2 ## Install behavior - Post-install hook: not defined - Bottle: available on arm64_linux, arm64_sequoia, arm64_sonoma, arm64_tahoe, sonoma, x86_64_linux ## Freshness - Page generated: 2026-07-08 - Package-manager version: 18-8cc5c - Local data: ok - Upstream repository: https://github.com/soedinglab/MMseqs2 - info: No package-manager update timestamp was available. - info: No cached GitHub release or tag data was available. ## Project history and usage MMseqs2, short for Many-against-Many sequence searching, is a bioinformatics suite from Martin Steinegger, Johannes Soding, and collaborators for searching and clustering very large protein and nucleotide sequence sets. The project README describes it as open-source C++ software for Linux, macOS, and Windows via Cygwin, built for multicore and multi-server scalability. Its 2017 Nature Biotechnology paper introduced MMseqs2 as a sensitive protein sequence search tool for massive datasets, and the project documentation frames it as much faster than BLAST while preserving high sensitivity at practical search settings. ### Project history Its major technical milestones followed the growth of public sequence databases. The 2018 Nature Communications Linclust paper integrated a linear-time clustering workflow into MMseqs2, demonstrating clustering of 1.6 billion metagenomic protein fragments in 10 hours on a single server and showing why quadratic or near-quadratic approaches such as CD-HIT and UCLUST struggled at that scale. A 2019 Bioinformatics paper expanded the ecosystem with an MMseqs2 desktop and local web-server app for interactive searches through custom protein sequence and profile databases, reducing query overhead and exposing MMseqs2 to users outside command-line-only workflows. ### How it is used In practice, users run the `mmseqs` executable as a suite of modules and workflows: creating MMseqs2 databases from FASTA or FASTQ, running `easy-search` for sequence search, `easy-cluster` for cascaded clustering, `easy-linclust` for larger datasets, converting alignment results, and using GPU-backed search modes where available. Its package-manager niche is scientific computing rather than general CLI tooling: Homebrew, Debian, Ubuntu, and Nix packages make a research-grade sequence analysis engine available to workstation and server users without building the full C++ stack by hand. ### Sources - - - - - - ## Security Notes infrastructure mutation or orchestration signal. - **Geiger risk:** orange / medium - infrastructure mutation or orchestration signal ## Source Database Details - **Source Database:** Homebrew formula API - **Tap:** homebrew/core - **Full Name:** mmseqs2 - **Version Scheme:** 0 - **Revision:** 0 - **Head Version:** HEAD - **Bottle Stable Root URL:** - **Deprecated:** no - **Disabled:** no - **Keg Only:** no - **URL Keys:** head, stable ## Other Package-Manager Records - Debian apt - mmseqs2 - 15-6f452+ds-2+b3: normalized package name match | Debian stable package indexes: mmseqs2 from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | ultra fast and sensitive protein search and clustering | https://github.com/soedinglab/MMseqs2 - Debian apt - mmseqs2-examples - 15-6f452+ds-2: normalized package name match | Debian stable package indexes: mmseqs2-examples from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | optional resources for the mmseqs2 package | https://github.com/soedinglab/MMseqs2 - Nix - mmseqs2: normalized package name match | nixpkgs package indexes: pkgs/by-name/mm/mmseqs2/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1 - Ubuntu apt - mmseqs2 - 15-6f452+ds-2: normalized package name match | Ubuntu 24.04 LTS package indexes: mmseqs2 from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | ultra fast and sensitive protein search and clustering | https://github.com/soedinglab/MMseqs2 - Ubuntu apt - mmseqs2-examples - 15-6f452+ds-2: normalized package name match | Ubuntu 24.04 LTS package indexes: mmseqs2-examples from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | optional resources for the mmseqs2 package | https://github.com/soedinglab/MMseqs2 ## Related links - [Secret-risk packages](https://www.automicvault.com/pkg/secret-risk-packages/) - Has protected-tool coverage, approval-gate, or non-low Geiger security signals. - [Terminal utility packages](https://www.automicvault.com/pkg/terminal-utilities/) - Matched terminal and command-line workflow metadata. - [Text processing packages](https://www.automicvault.com/pkg/text-processing-tools/) - Matched text, document, or structured-data processing metadata. - [Networking and protocol packages](https://www.automicvault.com/pkg/networking-protocol-tools/) - Matched network, protocol, or remote-service metadata. - [wget](https://www.automicvault.com/pkg/brew/wget/) - Runtime dependency declared by Homebrew. - [cmake](https://www.automicvault.com/pkg/brew/cmake/) - Build dependency declared by Homebrew. - [hmmer](https://www.automicvault.com/pkg/brew/hmmer/) - Shares av.db curated category or tags: bioinformatics, cli, science, sequence-analysis, sequence-search. - [seqkit](https://www.automicvault.com/pkg/brew/seqkit/) - Shares av.db curated category or tags: bioinformatics, cli, science, sequence-analysis. - [seqtk](https://www.automicvault.com/pkg/brew/seqtk/) - Shares av.db curated category or tags: bioinformatics, cli, science, sequence-analysis. - [kraken2](https://www.automicvault.com/pkg/brew/kraken2/) - Shares av.db curated category or tags: bioinformatics, cli, metagenomics, science. - [paml](https://www.automicvault.com/pkg/brew/paml/) - Shares av.db curated category or tags: bioinformatics, cli, protein-sequences, science. - [ropebwt3](https://www.automicvault.com/pkg/brew/ropebwt3/) - Shares av.db curated category or tags: bioinformatics, cli, science, sequence-search. - [skani](https://www.automicvault.com/pkg/brew/skani/) - Shares av.db curated category or tags: bioinformatics, cli, metagenomics, science. - [spades](https://www.automicvault.com/pkg/brew/spades/) - Shares av.db curated category or tags: bioinformatics, cli, metagenomics, science. - [kalign](https://www.automicvault.com/pkg/brew/kalign/) - Local package facts share a topical domain. Shared terms: analysis, bioinformatics, cli, fast, libomp. ## Combined YAML source View the package source record on GitHub. [combined/mmseqs2.yml](https://github.com/automic-vault/db/blob/main/combined/mmseqs2.yml) ## Sources - Nucleus package database - Geiger risk classifier - package-page enrichment - curated package history - package version freshness - av.db category and tag curation - package relationship graph - external package-manager database matches - cross-ecosystem install command graph